a-slide / pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

Home Page:https://a-slide.github.io/pycoQC/

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Implement BRI instead of pysam for BAM reading

a-slide opened this issue · comments

The current pysam method load the entire bam file in memory.
Using Jared's bri package would allow to load reads one at the time => https://github.com/jts/bri
Using the ONT python wrapper is probably the easiest way to go: https://github.com/nanoporetech/bripy